From 5040b9b0b3ede45905b7397676f13e5aa020d237 Mon Sep 17 00:00:00 2001
From: "Brenton M. Wiernik" <bwiernik@users.noreply.github.com>
Date: Sun, 23 Jul 2023 15:02:27 -0400
Subject: [PATCH] Update check_model() defaults to align with
 https://github.com/easystats/see/pull/299

Also change default to `verbose = FALSE`
---
 DESCRIPTION            | 1 +
 R/check_model.R        | 9 +++++----
 R/check_normality.R    | 2 +-
 man/check_model.Rd     | 9 +++++----
 man/check_normality.Rd | 2 +-
 5 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 50e2387ac..474728a98 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -124,6 +124,7 @@ Suggests:
     patchwork,
     pscl,
     psych,
+    qqplotr (>= 0.0.6),
     randomForest,
     rmarkdown,
     rstanarm,
diff --git a/R/check_model.R b/R/check_model.R
index 0822bcadc..1ea9bd909 100644
--- a/R/check_model.R
+++ b/R/check_model.R
@@ -27,13 +27,14 @@
 #'   for dots, and third color for outliers or extreme values.
 #' @param theme String, indicating the name of the plot-theme. Must be in the
 #'   format `"package::theme_name"` (e.g. `"ggplot2::theme_minimal"`).
-#' @param detrend Should QQ/PP plots be detrended?
+#' @param detrend Logical. Should Q-Q/P-P plots be de-trended?
+#'   Defaults to `TRUE` if the *qqplotr* package is installed and `FALSE` otherwise.
 #' @param show_dots Logical, if `TRUE`, will show data points in the plot. Set
 #'   to `FALSE` for models with many observations, if generating the plot is too
 #'   time-consuming. By default, `show_dots = NULL`. In this case `check_model()`
 #'   tries to guess whether performance will be poor due to a very large model
 #'   and thus automatically shows or hides dots.
-#' @param verbose Toggle off warnings.
+#' @param verbose If `FALSE` (default), suppress most warning messages.
 #' @param ... Currently not used.
 #' @inheritParams check_predictions
 #'
@@ -174,11 +175,11 @@ check_model.default <- function(x,
                                 dot_alpha = 0.8,
                                 colors = c("#3aaf85", "#1b6ca8", "#cd201f"),
                                 theme = "see::theme_lucid",
-                                detrend = FALSE,
+                                detrend = requireNamespace("qqplotr", quietly = TRUE),
                                 show_dots = NULL,
                                 bandwidth = "nrd",
                                 type = "density",
-                                verbose = TRUE,
+                                verbose = FALSE,
                                 ...) {
   # check model formula
   if (verbose) {
diff --git a/R/check_normality.R b/R/check_normality.R
index 0f26a557d..b5b658b5e 100644
--- a/R/check_normality.R
+++ b/R/check_normality.R
@@ -24,7 +24,7 @@
 #' (e.g. Q-Q plots) are preferable. For generalized linear models, no formal
 #' statistical test is carried out. Rather, there's only a `plot()` method for
 #' GLMs. This plot shows a half-normal Q-Q plot of the absolute value of the
-#' standardized deviance residuals is shown (being in line with changes in
+#' standardized deviance residuals is shown (in line with changes in
 #' `plot.lm()` for R 4.3+).
 #'
 #' @examples
diff --git a/man/check_model.Rd b/man/check_model.Rd
index 325e9ec07..18a1d6075 100644
--- a/man/check_model.Rd
+++ b/man/check_model.Rd
@@ -17,11 +17,11 @@ check_model(x, ...)
   dot_alpha = 0.8,
   colors = c("#3aaf85", "#1b6ca8", "#cd201f"),
   theme = "see::theme_lucid",
-  detrend = FALSE,
+  detrend = requireNamespace("qqplotr", quietly = TRUE),
   show_dots = NULL,
   bandwidth = "nrd",
   type = "density",
-  verbose = TRUE,
+  verbose = FALSE,
   ...
 )
 }
@@ -55,7 +55,8 @@ for dots, and third color for outliers or extreme values.}
 \item{theme}{String, indicating the name of the plot-theme. Must be in the
 format \code{"package::theme_name"} (e.g. \code{"ggplot2::theme_minimal"}).}
 
-\item{detrend}{Should QQ/PP plots be detrended?}
+\item{detrend}{Logical. Should Q-Q/P-P plots be de-trended?
+Defaults to \code{TRUE} if the \emph{qqplotr} package is installed and \code{FALSE} otherwise.}
 
 \item{show_dots}{Logical, if \code{TRUE}, will show data points in the plot. Set
 to \code{FALSE} for models with many observations, if generating the plot is too
@@ -74,7 +75,7 @@ to a different value.}
 options are appropriate for models with discrete - binary, integer or ordinal
 etc. - outcomes).}
 
-\item{verbose}{Toggle off warnings.}
+\item{verbose}{If \code{FALSE} (default), suppress most warning messages.}
 }
 \value{
 The data frame that is used for plotting.
diff --git a/man/check_normality.Rd b/man/check_normality.Rd
index 69f3b273d..b6591cc1d 100644
--- a/man/check_normality.Rd
+++ b/man/check_normality.Rd
@@ -33,7 +33,7 @@ significant results for the distribution of residuals and visual inspection
 (e.g. Q-Q plots) are preferable. For generalized linear models, no formal
 statistical test is carried out. Rather, there's only a \code{plot()} method for
 GLMs. This plot shows a half-normal Q-Q plot of the absolute value of the
-standardized deviance residuals is shown (being in line with changes in
+standardized deviance residuals is shown (in line with changes in
 \code{plot.lm()} for R 4.3+).
 }
 \note{